annotate IMSAME/src/structs.h @ 3:09d02332c84c draft

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#ifndef STRUCTS_H
#define STRUCTS_H

#include <inttypes.h>

//Structs required for the dotplot workflow
#define MAXLID 200
//#define READBUF 2000000000 //2 GB
#define READBUF 500000000 //500MB
#define INITSEQS 3000 //Number of starting sequences (in database)
#define POINT 4

#define FIXED_K 12

#define MAXLID 200
#define ALIGN_LEN 60 //For NW alignment
#define MAX_READ_SIZE 10000 //Maximum length of read to have a portion of the table allocated
#define MAX_WINDOW_SIZE 1000 //Maximum window length to explore NW table
//#define POOL_SIZE 2500000000 // by 16 bytes it is 40 GB
#define POOL_SIZE 12500000 // 1 GB if 16 bytes
#define MAX_MEM_POOLS 128 
#define FIXED_LOADING_THREADS 4

#define FALSE 0
#define TRUE 1

extern uint64_t custom_kmer;

typedef char _vector_char __attribute__ ((vector_size (32*sizeof(char))));

//Struct for linked list of positions
typedef struct linked_list_pos{
    uint64_t pos;
    uint64_t s_id;
    //uint64_t extended_hash;
    struct linked_list_pos * next;
} llpos;

typedef struct AVL_Node{
    uint64_t key;
    struct AVL_Node * left;
    struct AVL_Node * right;
    uint64_t height;
    uint64_t count;
    llpos * next;
} AVLTree;

//Struct for memory pool por lists
typedef struct mempool_l{
    llpos * base;
    uint64_t current;
} Mempool_l;

//Struct for memory pool por AVLtree
typedef struct mempool_AVL{
    AVLTree * base;
    uint64_t current;
} Mempool_AVL;


//Struct for a whole sequence(s) data
typedef struct seqinfo{
    unsigned char * sequences;
    uint64_t * start_pos;
    uint64_t total_len;
    uint64_t n_seqs;
} SeqInfo;

//Struct for the alignment of a quick hit
typedef struct quickfrag{
    uint64_t x_start;
    uint64_t y_start;
    uint64_t t_len;
    long double coverage;
    long double e_value;
} Quickfrag;

typedef struct point{
    uint64_t x;
    uint64_t y;
} Point;

typedef struct container{
    llpos * table[4][4][4][4][4][4][4][4][4][4][4]; // One reduced; A,C,G,T tables in use
} Container;

typedef struct AVLcontainer{
    AVLTree root[4][4][4][4][4][4][4][4][4][4][4];
} AVLContainer;

typedef struct{
    char * temp_seq_buffer;
    SeqInfo * data_database;
    uint64_t t_len;
    uint64_t word_size;
    uint64_t read_from;
    uint64_t read_to;
    uint64_t contained_reads;
    uint64_t base_coordinates;
    uint64_t n_allocs;
    char thread_id;
    AVLContainer * ct;
    Mempool_l * mp;
    uint64_t n_pools_used;
    uint64_t n_pools_used_AVL;
    Mempool_AVL * mp_AVL;
} LoadingDBArgs;

struct cell{
    int64_t score;
    uint64_t xfrom;
    uint64_t yfrom;
};

struct positioned_cell{
    int64_t score;
    uint64_t xpos;
    uint64_t ypos;
};

struct best_cell{
    struct positioned_cell c;
    uint64_t j_prime;
};

typedef struct{
    uint64_t identities;
    uint64_t length;
    uint64_t igaps;
    uint64_t egaps;
} BasicAlignment;

typedef struct queue{
    uint64_t r1; //reads region
    uint64_t r2;
    struct queue * next;
} Queue;

typedef struct{
    Queue * head;
} Head;


#endif